Protein target profile

KP13_00862

Histidyl-tRNA synthetase

Genome: KpKP13 Gene: AHE43225.1 hisS 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H1G0
Length 424
Pocket druggability 0.645
Direct ligand evidence 0 53 total records
Functional annotation 1 EC 4 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
25.269 Lower values reduce human off-target concern.
Human E-value
6.26e-11
Gut microbiome similarity
5.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
91.509 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
94.93 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.645
Structure A0A0H3H1G0
Pocket Pocket 6
P2Rank 0.87
Structure A0A0H3H1G0
Pocket Pocket 1
ColabFold model
FPocket 0.375 · Pocket 15
P2Rank 0.835 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 266 / 4744 genomes with a hit
Prevalence 5.6%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

Primary amino-acid sequence viewer.

MAKNIQAIRGMNDYLPGETALWQRIEGSLKQVLGSYGYSEIRLPIVEQTPLFKRAIGEVTDVVEKEMYTFEDRNGDSLTLRPEGTAGCVRAGIEHGLLYNQEQRLWYVGPMFRHERPQKGRYRQFHQIGAEVFGLQGPDIDAELIMLTARWWRELGISEHVSLELNSIGSLEARANYRDALVAYLEQFTDKLDEDSKRRMYTNPLRVLDSKNPDVQALLNDAPALGDYLDEESKAHFAGLCALLDDAGIRYTVNQRLVRGLDYYNRTVFEWVTTSLGSQGTVCAGGRYDGLVEQLGGRATPGVGFAMGLERLVLLVQAVNPEFKADPVVDIYLVASGTDTQSAAMRLAEQVRDALPGVKLMTNHGGGNFKKQFARADKWGARVALVVGESEIADGNVVVKDLRSGEQTTVTQESVAAHLRTLLG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0004821 Catalysis of the reaction: ATP + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His).
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0006427 The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. The histidyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3''-OH group of a histidine-accetping tRNA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
328 420 CDD cd00859 HisRS_anticodon
328 420 InterPro IPR033656 Histidyl-anticodon-binding
326 423 Gene3D G3DSA:3.40.50.800 -
326 423 InterPro IPR036621 Anticodon-binding domain superfamily
18 317 CDD cd00773 HisRS-like_core
18 317 InterPro IPR041715 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain
2 323 FunFam G3DSA:3.30.930.10:FF:000005 Histidine--tRNA ligase
5 318 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases
5 318 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
10 312 Pfam PF13393 Histidyl-tRNA synthetase
10 312 InterPro IPR041715 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain
326 423 FunFam G3DSA:3.40.50.800:FF:000007 Histidine--tRNA ligase
338 420 Pfam PF03129 Anticodon binding domain
338 420 InterPro IPR004154 Anticodon-binding
1 423 PIRSF PIRSF001549 His-tRNA_synth
1 423 InterPro IPR004516 Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit
2 322 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
2 322 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
329 423 SUPERFAMILY SSF52954 Class II aaRS ABD-related
4 414 PANTHER PTHR43707 HISTIDYL-TRNA SYNTHETASE
4 414 InterPro IPR004516 Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit
6 411 NCBIfam TIGR00442 histidine--tRNA ligase
6 411 InterPro IPR015807 Histidine-tRNA ligase
1 327 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile.
1 327 InterPro IPR006195 Aminoacyl-tRNA synthetase, class II
3 421 Hamap MF_00127 Histidine--tRNA ligase [hisS].
3 421 InterPro IPR015807 Histidine-tRNA ligase

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #6
0.645
Show in viewer
Surrounding area
Site 2 FPocket #22
0.357
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.87
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Surrounding area
Site 2 P2Rank #2
0.115
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Surrounding area
Site 3 P2Rank #3
0.089
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.01
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:103-103
UniProt: Binding site:117-117
UniProt: Binding site:121-121
UniProt: Binding site:249-249
UniProt: Binding site:253-254
UniProt: Binding site:73-75
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3H1G0
AlphaFold DB full sequence Viewing
ColabFold KP13_00862
ColabFold full sequence Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
HAM PDB via homolog 484.4 Da · LogP -3.37 · TPSA 251.3 Open detail RCSB PDB
HSO PDB via homolog Detail RCSB PDB
HSS PDB via homolog Detail RCSB PDB
ZINC1083817667 ZINC proposed compound · Tanimoto 0.716 Detail ZINC
ZINC936069053 ZINC proposed compound · Tanimoto 0.716 Detail ZINC

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
HAM RCSB PDB P60906 484.4 Da LogP -3.37 TPSA 251.3 1 viol. ✓ Clean c1c(nc[nH]1)C[C@@H](C(=O)O[P@](=O)([O-])OC[C@@H…
HSO RCSB PDB P60906 142.2 Da LogP -1.31 TPSA 76.2 ✓ Ro5 ✓ Clean c1c([nH+]c[nH]1)C[C@@H](CO)N
HSS RCSB PDB P60906 483.5 Da LogP -3.30 TPSA 246.5 2 viol. ✓ Clean c1c([nH]cn1)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@…

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.